Probiotic bacteria improve fermentation in the large intestine through interaction with indigenous bacteria. The microflora in the large intestine differ from one individual to another. The objective of this study was to determine whether the different cecal microflora induce different probiotic effects on cecal fermentation in three pigs (pig A, B and C). Pigs were administered fermented milk prepared with the Lactobacillus casei strain Shirota (LCS) as a probiotic for 2 wk. The average number of LCS was higher than 5.0 (log cfu/g cecal digesta) in all pigs. The hierarchical clustering of the temperature-gradient gel electrophoresis (TGGE) profile of cecal bacteria showed that the cecal microflora was slightly altered by the LCS dose in all pigs. However, the molar ratios of cecal butyrate in pigs A and C were significantly increased by LCS. Inversely, the molar ratio of propionate in pigs A and C was significantly decreased by LCS. However, the molar ratio of individual short-chain fatty acid in pig B was not significantly affected by LCS. The hierarchical clustering of the TGGE profiles indicated that the cecal microflora of pig A resembled that of pig C and that of pig B was dissimilar to those of pigs A and C. These results indicated that the effect of LCS on fermentation in the large intestine was possibly dependent on the composition of indigenous microflora.